- Fixed the example in the mkinmod documentation

- Fixed the vignette
- Did not fix the unit tests for mkinmod yet



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@31 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

3 files changed, 21 insertions, 14 deletions

diff --git a/TODO b/TODO
index 13bc6fc..a49957d 100644
--- a/TODO
+++ b/TODO
@@ -1,9 +1,12 @@
-- Fix transformation and backtransformation of formation fractions
-- Fix problems with the schaefer complex test data (test.R)
+Must have:
+- Fix remaining problem with the schaefer complex test data (test.R)
+- Fix parent only SFORB model (see vignette)
+- Fix unit tests for mkinmod
 - Adapt mkinplot function
+
+Nice to have:
 - Calculate confidence intervals for parameters assuming normal distribution
 - Calculate confidence intervals for DT50 and DT90 values when only one parameter is involved
-- Fix DT50 and DT90 calculation for SFORB_SFO
 - Add unit tests for mkinfit
 - Document validation against fits documented in chapter 13 of FOCUS (2006)
 - Reproduce example anaylses (L1, L2, ...) in FOCUS (2006)
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index af37f7c..aaa77e6 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -54,10 +54,16 @@ mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_
 }
 \examples{
   SFO <- mkinmod(degradinol = list(type = "SFO"))
-  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, solution_type = "analytical")
-  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, solution_type = "eigen")
-  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, atol = 1e-20)
-  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, atol = 1e-20, method = "rk4")
-  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), (1:200)/10)
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "analytical")
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "eigen")
+
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20, solution_type = "analytical")[20,]
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20)[20,]
+  # The integration method does not make a lot of difference
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, method = "bdf")[20,]
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, method = "rk4")[20,]
+  # The number of output times does make a lot of difference
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), seq(0, 20, by = 0.1))[201,]
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), seq(0, 20, by = 0.01))[2001,]
 }
 \keyword{ manip }
diff --git a/vignettes/mkin.Rnw b/vignettes/mkin.Rnw
index 1eebd44..ee472ba 100644
--- a/vignettes/mkin.Rnw
+++ b/vignettes/mkin.Rnw
@@ -147,14 +147,12 @@ on the fundamental system of the coefficient matrix, as proposed by
 <<model_fitting, echo=TRUE>>=

 SFO.fit <- mkinfit(SFO, FOCUS_2006_C)

 summary(SFO.fit)

-SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)

-summary(SFORB.fit)

+#SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)

+#summary(SFORB.fit)

 SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D, plot=TRUE)

 summary(SFO_SFO.fit, data=FALSE)

-#SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D, 

-#  parms.ini = c(f_parent_to_m1 = 0.5, k_m1 = 0.2), 

-#  plot=TRUE)

-#summary(SFORB_SFO.fit, data=FALSE)

+SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D, plot=TRUE)

+summary(SFORB_SFO.fit, data=FALSE)

 @

 

 \bibliographystyle{plainnat}